maybe you could boot to 'Always Fresh' again -> set your network -> run 'changes-time' script to catch latest updates to the filesystem?
it should help you identify which files needs to be included in /rootcopy

If you use fat or ntfs then you lost file permissions. If you must use rootcopy then
try: copy /etc/rc.d/rc.local to rootcopy, edit rc.local and add commands to set correct permissions for needed folders/files.
Easier way is to create little save.dat.xzm file -> mount and copy here needed file -> move this file to base folder or -> use for storing changes but with changes-ro (or EXIT: + edit changes-exit.conf) cheatcode then you can modify them (persistant) in /mnt/live/memory/images/save.dat.xzm or /mnt/live/memory/images/changes. Probably too complicated in words.